I would like to use data from https://portal.brain-map.org/atlases-and-data/rnaseq/human-m1-10x and https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-10x. I am very new to single cell RNA sequencing. I was trying to use Seurat to do the analysis. I started to read the matrix file, its taking a very long time to read this file into R as it is 68GB. I tried using server with 256GB RAM. I would like to know if this is normal. Is there any other better way to do the t-SNE plots (cluster by cell type) with exon expression data for a list of genes?
Please let me know.
Hi @santhi. Sorry for the delay in responding to this post. We recognize that there are some challenges for reading these large files. I’d suggest starting with previous forum topics which discuss reading such files in R and in python. It is also worth noting that we provide t-SNE coordinates as part of the relevant “Download” links. For most data sets (especially 10X) we do not separate exonic from intronic reads.
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